Massarray rt software version 3

Manufactured by Labcorp

The MassARRAY RT software version 3.0.0.4 is a software tool designed for the analysis of genetic data. It provides functionality for data acquisition, processing, and reporting from the MassARRAY system.

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Lab products found in correlation

Massarray typer software version 3, by Labcorp (5 mentions) Massarray system, by Labcorp (4 mentions) Massarray nanodispenser, by Labcorp (2 mentions) Tianamp blood dna kit, by Tiangen Biotech (2 mentions) Qiamp blood kit, by Qiagen (1 mentions) Iplex gold chemistry, by Labcorp (1 mentions) Dna extraction kit, by Takara Bio (1 mentions) Assay designer software package, by Labcorp (1 mentions) 384 well spectrochip, by Labcorp (1 mentions) Ezna tm blood dna midi kit, by Omega Bio-Tek (1 mentions) Spectrochip, by Labcorp (1 mentions) Iplex enzyme, by Labcorp (1 mentions) Massarray platform, by Labcorp (1 mentions) Hotstartaq dna polymerase, by Qiagen (1 mentions)

5 protocols using massarray rt software version 3

Genetic Variants Associated with POAG

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Genomic DNA was extracted from leukocytes of the peripheral blood for each participant. It was purified by the Qiagen QIAmp Blood Kit (Qiagen, Hilden, Germany). Fourteen previously reported SNPs were chosen for genotyping, including rs1900004, rs3858145, rs7916697 at ATOH7, rs10116277, rs1063192, rs2157719, rs4977756, rs523096, rs7049105 at CDKN2B-AS1, rs33912345, and rs10483727 at SIX1/SIX6, rs4656461, and rs7555523 at TMCO1, as well as rs1192415 at TGFEB3-CDC7. The SNPs included in this study were either tagging SNPs referenced to HapMap database or representative SNPs reported significantly associated with development of POAG in previous publications (Burdon et al., 2011 (link), 2012 (link); Fan et al., 2011 (link); Khor et al., 2011 (link); Ramdas et al., 2011 (link); Wiggs et al., 2012 (link); Li et al., 2015 (link)).
Single nucleotide polymorphism genotyping was performed using iPLEX Gold chemistry on the MassARRAY system (Sequenom, Inc., San Diego, CA, United States) by means of matrix assisted laser desorption ionization time-of-flight mass spectrometry method (MALDI-TOF) according to the manufacturer’s instructions. Genotype calling was performed in real time with MassARRAY RT software version 3.0.0.4 and analyzed using the MassARRAY Typer software version 3.4 (Sequenom). Each SNP with call rate greater than 95% was analyzed in the next step.

Chen Y., Qiu C., Qian S., Chen J., Chen X., Wang L, & Sun X. (2018). Lack of Association of rs1192415 in TGFBR3-CDC7 With Visual Field Progression: A Cohort Study in Chinese Open Angle Glaucoma Patients. Frontiers in Genetics, 9, 488.

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SNP Genotyping in Chinese Population

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Tag SNPs were chosen from the genotyped SNPs in the Han Chinese population (HCB) of the HapMap project (the Phase I database). The candidate’s SNPs were restricted to minor allele frequencies larger than 15%. Genomic DNA used for polymerase chain reaction (PCR) amplification was extracted from a whole blood sample using a DNA extraction kit (Takara, China) according to the manufacturer’s instructions. Primers for amplification were designed with AssayDesigner 3.1 software. The sequences of primers for amplification of the four loci in the SLC22A3 and LPA genes are listed in Table 1. SNP genotyping was conducted using the MassARRAY system (Sequenom) by means of the matrix-assisted laser desorption ionization time of flight mass spectrometry method (MALDI-TOF) according to the manufacturer’s instructions (Bio Miao Biological technology (Beijing) Co., Ltd). Genotype calling was performed in real-time with MassARRAY RT software version 3.0.0.4 and analyzed using the MassARRAY Typer software version 3.4 (Sequenom). As quality controls, 5% - 10% of the samples were genotyped in duplicate, and no inconsistencies were observed. Controls distributed in each 384-well plate were also checked for consistency. Cluster plots were made from the low and the high mass allele signals.

Song Z.K., Cao H.Y., Wu H.D., Zhou L.T, & Qin L. (2016). A Case-Control Study of the Relationship Between SLC22A3-LPAL2-LPA Gene Cluster Polymorphism and Coronary Artery Disease in the Han Chinese Population. Iranian Red Crescent Medical Journal, 18(6), e35387.

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Genomic DNA Extraction and SNP Genotyping

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Three to five milliliters of peripheral blood was collected in tubes coated with EDTA. Genomic DNA was extracted from the leukocytes in the blood using the EZNA TM Blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA), according to the manufacturer protocol. Primers for PCR and single-base extension were designed by using the Assay Designer software package (Sequenom Inc., San Diego, CA, USA). SNP genotyping was performed by Shanghai Benegene Biotechnology Co., Ltd. (Shanghai, China) using the MassARRAY system (Sequenom) by means of matrix-assisted laser desorption ionization-time of flight mass spectrometry method (MALDI-TOF) according to manufacturer instructions. The completed genotyping reactions were spotted onto a 384-well spectroCHIP (Sequenom) using the MassARRAY Nanodispenser (Sequenom) and determined by MALDI-TOF. Genotype calling was performed in real-time with the MassARRAY RT software version 3.0.0.4 and analyzed using the MassARRAY Typer software version 3.4 (Sequenom).

He Q.S., Yang L.F., Wang W.B., Yuan B., Zhang L.Y, & Guo X.J. (2015). Vascular endothelial growth factor gene is associated with hypertensive cerebellar hemorrhage and rehabilitative treatment. Genetics and molecular research : GMR, 14(3).

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Genotyping of SNPs Using MassARRAY

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Peripheral blood (3-5 mL) was collected from the subjects and preserved in tubes coated with ethylenediaminetetraacetic acid. Genomic DNA was extracted using a TIANamp Blood DNA Kit (TIANGEN Biotech, Beijing, China) and stored at -4°C until use. Genotyping was carried out for all SNPs using the MassARRAY platform (Sequenom Inc., San Diego, CA, USA). Primer extension and polymerase chain reaction were performed according to the manufacturer instructions, using iPLEX enzyme (Sequenom Inc.) and HotStarTaq DNA polymerase (Qiagen, Hilden, Germany). The completed genotyping reactions were spotted onto a 384-well SpectroCHIP (Sequenom Inc.) using a MassARRAY Nanodispenser (Sequenom Inc.), and determined by a matrix-assisted laser desorption ionization time-of-flight mass spectrometer. Genotype calling was performed in real-time with the MassARRAY RT software version 3.0.0.4 and analyzed using the MassARRAY Typer software version 3.4 (Sequenom Inc.).

Chen L.P., Cai P.S, & Liang H.B. (2015). Association of the genetic polymorphisms of NFKB1 with susceptibility to ovarian cancer. Genetics and molecular research : GMR, 14(3).

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SNP Genotyping Using MALDI-TOF MS

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Peripheral blood (3-5 mL) was collected from each participant and placed in ethylenediaminetetraacetic acid-containing specimen tubes. Genomic DNA was extracted using a TIANamp Blood DNA Kit (TIANGEN, Beijing, China) and then stored at -20°C until required. SNP genotyping was performed using matrix-assisted laser desorption ionizationtime of flight mass spectrometry (MALDI-TOF MS) (MassARRAY system, Sequenom Inc., San Diego, CA, USA). Primers were designed using the Sequenom software, and the extension reaction produced allele-specific products with masses differing by 30 Da, or approximately the size of one single nucleotide. Primer extension and polymerase chain reaction (PCR) were performed according to the manufacturer instructions. Genotype calling was performed in real-time using the MassARRAY RT software version 3.0.0.4 and data analysis was performed using the MassARRAY Typer software version 3.4 (Sequenom Inc.).

Xu E.D., Xiao Y.F., Wang J.J, & Dong L. (2016). Association study between matrix metalloproteinase-9 gene (MMP9) polymorphisms and the risk of Henoch-Schönlein purpura in children. Genetics and molecular research : GMR, 15(2).

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